YBAK_HAEIN
ID YBAK_HAEIN Reviewed; 158 AA.
AC P45202; Q9RP30;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 21-FEB-2001, sequence version 2.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK;
DE EC=4.2.-.-;
GN Name=ybaK; OrderedLocusNames=HI_1434;
OS Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=71421;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=7542800; DOI=10.1126/science.7542800;
RA Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT Rd.";
RL Science 269:496-512(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RA Bonander N., Eisenstein E.;
RL Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP FUNCTION IN CYS-TRNA(PRO) EDITING, AND MUTAGENESIS OF LYS-46.
RX PubMed=15322138; DOI=10.1074/jbc.c400304200;
RA An S., Musier-Forsyth K.;
RT "Trans-editing of Cys-tRNAPro by Haemophilus influenzae YbaK protein.";
RL J. Biol. Chem. 279:42359-42362(2004).
RN [4]
RP FUNCTION AS A DEACYLASE, AND SUBSTRATE SPECIFICITY.
RX PubMed=15886196; DOI=10.1074/jbc.m502174200;
RA Ruan B., Soll D.;
RT "The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase.";
RL J. Biol. Chem. 280:25887-25891(2005).
RN [5]
RP SUBUNIT.
RX PubMed=16087664; DOI=10.1074/jbc.m507550200;
RA An S., Musier-Forsyth K.;
RT "Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel
RT synthetase.YbaK.tRNA ternary complex.";
RL J. Biol. Chem. 280:34465-34472(2005).
RN [6]
RP FUNCTION, REACTION MECHANISM, SUBSTRATE SPECIFICITY, AND MUTAGENESIS OF
RP TYR-20; PHE-29; LYS-46; THR-47; GLY-101; SER-129; GLY-131; GLY-134 AND
RP SER-136.
RX PubMed=21768119; DOI=10.1074/jbc.m111.232611;
RA So B.R., An S., Kumar S., Das M., Turner D.A., Hadad C.M.,
RA Musier-Forsyth K.;
RT "Substrate-mediated fidelity mechanism ensures accurate decoding of proline
RT codons.";
RL J. Biol. Chem. 286:31810-31820(2011).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RX PubMed=10813833;
RX DOI=10.1002/(sici)1097-0134(20000701)40:1<86::aid-prot100>3.0.co;2-y;
RA Zhang H., Huang K., Li Z., Banerjei L., Fisher K.E., Grishin N.V.,
RA Eisenstein E., Herzberg O.;
RT "Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at
RT 1.8-A resolution: functional implications.";
RL Proteins 40:86-97(2000).
CC -!- FUNCTION: Functions in trans to edit the amino acid from incorrectly
CC charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. Probably
CC compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Is also
CC able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity
CC in vitro against Gly-tRNA(Gly), as well as, at higher concentrations,
CC some other correctly charged tRNAs. Does not cleave Pro-tRNA(Pro).
CC {ECO:0000269|PubMed:15322138, ECO:0000269|PubMed:15886196,
CC ECO:0000269|PubMed:21768119}.
CC -!- SUBUNIT: May form a tertiary complex with ProRS and tRNA(Pro), as it
CC can be cross-linked to E.coli ProRS and to E.coli tRNA(Pro) in vitro.
CC It cannot compete with Ef-Tu for aminoacyl-tRNA binding, suggesting it
CC acts before release of the charged aminoacyl-tRNA from the synthetase.
CC {ECO:0000269|PubMed:16087664}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- MISCELLANEOUS: Reaction mechanism involves exclusion of catalytic water
CC from the active site and substrate-mediated catalysis: the sulfhydryl
CC side chain of the Cys substrate acts as a nucleophile and attacks the
CC carbonyl center of the ester bond, leading to the cleavage of the Cys-
CC tRNA ester bond and formation of a cyclic cysteine thiolactone
CC intermediate. In contrast, the INS editing domain of ProRS catalyzes
CC Ala-tRNA(Pro) hydrolysis via nucleophilic attack by a catalytic water
CC molecule (PubMed:21768119). {ECO:0000305|PubMed:21768119}.
CC -!- SIMILARITY: Belongs to the prolyl-tRNA editing family. YbaK/EbsC
CC subfamily. {ECO:0000305}.
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DR EMBL; L42023; AAC23081.1; -; Genomic_DNA.
DR EMBL; AF174386; AAD54290.1; -; Genomic_DNA.
DR PIR; H64171; H64171.
DR RefSeq; NP_439583.1; NC_000907.1.
DR PDB; 1DBU; X-ray; 1.80 A; A=1-158.
DR PDB; 1DBX; X-ray; 1.80 A; A/B=1-158.
DR PDBsum; 1DBU; -.
DR PDBsum; 1DBX; -.
DR AlphaFoldDB; P45202; -.
DR SMR; P45202; -.
DR STRING; 71421.HI_1434; -.
DR EnsemblBacteria; AAC23081; AAC23081; HI_1434.
DR KEGG; hin:HI_1434; -.
DR PATRIC; fig|71421.8.peg.1491; -.
DR eggNOG; COG2606; Bacteria.
DR HOGENOM; CLU_094875_1_1_6; -.
DR PhylomeDB; P45202; -.
DR BioCyc; HINF71421:G1GJ1-1457-MON; -.
DR EvolutionaryTrace; P45202; -.
DR Proteomes; UP000000579; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0043906; F:Ala-tRNA(Pro) hydrolase activity; IDA:UniProtKB.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR CDD; cd00002; YbaK_deacylase; 1.
DR Gene3D; 3.90.960.10; -; 1.
DR InterPro; IPR004369; Prolyl-tRNA_editing_YbaK/EbsC.
DR InterPro; IPR036754; YbaK/aa-tRNA-synt-asso_dom_sf.
DR InterPro; IPR007214; YbaK/aa-tRNA-synth-assoc-dom.
DR Pfam; PF04073; tRNA_edit; 1.
DR PIRSF; PIRSF006181; EbsC_YbaK; 1.
DR SUPFAM; SSF55826; SSF55826; 1.
DR TIGRFAMs; TIGR00011; YbaK_EbsC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Lyase; Protein biosynthesis; Reference proteome.
FT CHAIN 1..158
FT /note="Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK"
FT /id="PRO_0000168623"
FT SITE 29
FT /note="Participates in proton transfer during catalysis"
FT /evidence="ECO:0000250"
FT MUTAGEN 20
FT /note="Y->A: 45-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 29
FT /note="F->A: 29-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 46
FT /note="K->A: 66-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:15322138,
FT ECO:0000269|PubMed:21768119"
FT MUTAGEN 46
FT /note="K->I: 38-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:15322138,
FT ECO:0000269|PubMed:21768119"
FT MUTAGEN 46
FT /note="K->R: 44-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:15322138,
FT ECO:0000269|PubMed:21768119"
FT MUTAGEN 47
FT /note="T->A: 21-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 101
FT /note="G->A: 36-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 129
FT /note="S->A: 5.6-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 131
FT /note="G->A: 28-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 134
FT /note="G->A: 7.4-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 136
FT /note="S->A: 3.6-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT MUTAGEN 136
FT /note="S->H: 16-fold decrease in Cys-tRNA(Pro) deacylation
FT activity."
FT /evidence="ECO:0000269|PubMed:21768119"
FT CONFLICT 117
FT /note="N -> K (in Ref. 1; AAC23081)"
FT /evidence="ECO:0000305"
FT HELIX 3..11
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 32..37
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 41..43
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 44..52
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 58..65
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 72..78
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 89..96
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 118..122
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:1DBU"
FT HELIX 141..148
FT /evidence="ECO:0007829|PDB:1DBU"
FT STRAND 151..153
FT /evidence="ECO:0007829|PDB:1DBU"
SQ SEQUENCE 158 AA; 17155 MW; 45723E9DFC99535A CRC64;
MTPAIDLLKK QKIPFILHTY DHDPNNQHFG DEAAEKLGID PNRSFKTLLV AENGDQKKLA
CFVLATANML NLKKAAKSIG VKKVEMADKD AAQKSTGYLV GGISPLGQKK RVKTVINSTA
LEFETIYVSG GKRGLSVEIA PQDLAKVLGA EFTDIVDE
